8GIZ: E. coli clamp loader with open clamp

E. coli clamp loader with open clamp. Determined by electron microscopy at 2.7 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 2.7 Å
Organism: Escherichia coli K-12
Chains: 8
Atoms: 19,919
Mol. weight: 316.88 kDa
Ligands: AGS, MG, ZN
Released: 27 Mar 2024

Explore 8GIZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8GIZ contains 140 α-helices and 94 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 21 helices, 10 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	1
α-helix	6-8	3
α-helix	9-15	7
β-strand	20-25	6	1
α-helix	28-45	18
β-strand	51-54	4	1
α-helix	62-68	7
β-strand	72	1	2
β-strand	75	1	2
β-strand	79-83	5	1
α-helix	91-102	12
β-strand	109-114	6	1
α-helix	116-117	2
α-helix	119-122	4
α-helix	125-131	7
β-strand	134-139	6	1
α-helix	140-143	4
α-helix	146-157	12
β-strand	161-162	2	3
α-helix	164-173	10
α-helix	178-191	14
β-strand	196-197	2	3
α-helix	199-203	5
α-helix	214-223	10
α-helix	226-239	14
α-helix	243-263	21
α-helix	269-276	8
α-helix	280-282	3
α-helix	283-292	10
α-helix	300-313	14
α-helix	320-331	12

Chain B: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-43	4	4
α-helix	51-62	12
α-helix	77-84	8
β-strand	91-94	4	4
α-helix	101-111	11
β-strand	113	1	5
α-helix	114-115	2
β-strand	121-126	6	4
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-155	6	4
α-helix	164-167	4
β-strand	171-172	2	4
α-helix	179-193	15
α-helix	200-210	11
α-helix	214-228	15
α-helix	234-244	11
α-helix	248-258	11
α-helix	261-274	14
α-helix	278-297	20
α-helix	299-301	3
α-helix	310-319	10
α-helix	322-338	17
α-helix	339-341	3
α-helix	345-358	14
β-strand	360-361	2	6

Chain C: 24 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	15-17	3
α-helix	22-34	13
β-strand	40-44	5	7
α-helix	51-63	13
α-helix	77-84	8
β-strand	91-94	4	7
α-helix	101-109	9
α-helix	114-115	2
β-strand	121-126	6	7
α-helix	128-130	3
α-helix	133-144	12
β-strand	150-156	7	7
α-helix	159-161	3
α-helix	164-169	6
β-strand	171-174	4	7
α-helix	175-179	5
α-helix	180-193	14
β-strand	198	1	8
α-helix	200-209	10
α-helix	214-228	15
β-strand	232	1	8
α-helix	234-241	8
α-helix	246-258	13
α-helix	261-274	14
α-helix	278-297	20
α-helix	304-309	6
α-helix	310-319	10
α-helix	322-338	17
α-helix	345-358	14
α-helix	364-366	3

Chain D: 22 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	6-9	4
α-helix	22-34	13
β-strand	40-45	6	9
α-helix	51-63	13
α-helix	77-83	7
β-strand	91-94	4	9
α-helix	101-109	9
β-strand	113	1	10
α-helix	114-115	2
β-strand	123-126	4	9
α-helix	128-130	3
α-helix	133-144	12
β-strand	152-156	5	9
α-helix	164-169	6
β-strand	171-175	5	9
α-helix	176-179	4
α-helix	180-193	14
β-strand	198	1	11
α-helix	200-210	11
α-helix	214-227	14
β-strand	232	1	11
α-helix	234-241	8
α-helix	248-257	10
α-helix	261-274	14
α-helix	278-297	20
α-helix	299-301	3
α-helix	307-309	3
α-helix	310-319	10
α-helix	322-338	17
α-helix	345-358	14

Chain E: 20 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	7-19	13
β-strand	26-30	5	12
α-helix	37-49	13
α-helix	63-70	8
β-strand	77-79	3	12
β-strand	88	1	13
α-helix	90-100	11
β-strand	110-114	5	12
α-helix	117-119	3
β-strand	120	1	13
α-helix	122-133	12
α-helix	135-136	2
β-strand	139-145	7	12
α-helix	148-150	3
α-helix	153-158	6
β-strand	160-163	4	12
α-helix	169-179	11
α-helix	184-193	10
α-helix	200-206	7
α-helix	209-226	18
α-helix	229-231	3
α-helix	232-236	5
α-helix	241-260	20
α-helix	271-280	10
α-helix	283-302	20
α-helix	308-323	16
α-helix	327-330	4

Chain F: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	17-18	2	6

Chain H: 17 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	14
α-helix	7-18	12
α-helix	28-31	4
β-strand	32-38	7	15
β-strand	41-45	5	15
β-strand	51-58	8	15
β-strand	64	1	14
β-strand	66-71	6	15
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	14
β-strand	96-101	6	14
β-strand	104-109	6	14
β-strand	111	1	15
α-helix	122-124	3
β-strand	126-130	5	15
α-helix	132-141	10
α-helix	153-155	3
β-strand	158-164	7	5
β-strand	166-172	7	5
β-strand	177-182	6	5
β-strand	188-195	8	5
α-helix	196	1
α-helix	197-206	10
α-helix	213	1
β-strand	214-218	5	15
β-strand	222-227	6	15
β-strand	230-235	6	15
α-helix	236	1
β-strand	237	1	5
α-helix	241-243	3
β-strand	254-259	6	5
α-helix	260-273	14
α-helix	280-281	2
β-strand	282-286	5	16
β-strand	289-293	5	16
β-strand	304-306	3	16
β-strand	315-318	4	16
α-helix	321-330	10
β-strand	335-340	6	5
α-helix	347	1
β-strand	348-351	4	5
β-strand	357-360	4	5
α-helix	363-365	3

Chain I: 13 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-6	5	17
α-helix	7-10	4
α-helix	13-18	6
β-strand	33-38	6	18
β-strand	41-47	7	18
β-strand	51-58	8	18
β-strand	66-70	5	18
α-helix	72-81	10
α-helix	83	1
β-strand	87-93	7	17
β-strand	96-101	6	17
β-strand	104-109	6	17
β-strand	111	1	18
α-helix	113-115	3
β-strand	126-130	5	18
α-helix	132-142	11
α-helix	143-145	3
α-helix	153-155	3
β-strand	158-163	6	19
β-strand	166-172	7	19
β-strand	176-183	8	19
β-strand	191-195	5	19
α-helix	197-206	10
β-strand	214-218	5	18
β-strand	222-227	6	18
β-strand	230-235	6	18
α-helix	241-243	3
α-helix	244-247	4
β-strand	254-259	6	19
α-helix	260-271	12
β-strand	280-286	7	14
β-strand	289-294	6	14
β-strand	302-306	5	14
β-strand	309-310	2	19
β-strand	315-320	6	14
α-helix	321-331	11
β-strand	335-340	6	19
β-strand	347-350	4	19
β-strand	357-361	5	19
β-strand	364	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA polymerase III subunit delta	A	protein	343	Escherichia coli K-12	P28630 (AlphaFold model)
DNA polymerase III subunit tau	B, C, D	protein	431	Escherichia coli K-12	P06710 (AlphaFold model)
DNA polymerase III subunit delta'	E	protein	334	Escherichia coli K-12	P28631 (AlphaFold model)
DNA polymerase III subunit psi	F	protein	137	Escherichia coli K-12	P28632 (AlphaFold model)
Beta sliding clamp	H, I	protein	366	Escherichia coli K-12	P0A988

Sequence of entity 1 (A), FASTA

>8GIZ_1 DNA polymerase III subunit delta (chains A)
MIRLYPEQLRAQLNEGLRAAYLLLGNDPLLLQESQDAVRQVAAAQGFEEHHTFSIDPNTD
WNAIFSLCQAMSLFASRQTLLLLLPENGPNAAINEQLLTLTGLLHDDLLLIVRGNKLSKA
QENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCYEGNLLA
LAQALERLSLLWPDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHILQQLRLEG
SEPVILLRTLQRELLLLVNLKRQSAHTPLRALFDKHRVWQNRRGMMGEALNRLSQTQLRQ
AVQLLTRTELTLKQDYGQSVWAELEGLSLLLCHKPLADVFIDG

Sequence of entity 2 (B, C, D), FASTA

>8GIZ_2 DNA polymerase III subunit tau (chains B, C, D)
MSYQVLARKWRPQTFADVVGQEHVLTALANGLSLGRIHHAYLFSGTRGVGKTSIARLLAK
GLNCETGITATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDNVQYAPARGRF
KVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILSRCLQFHLKALDV
EQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTDQAIASGDGQVSTQAVSAM
LGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPA
ALGNDMAAIELRMRELARTIPPTDIQLYYQTLLIGRKELPYAPDRRMGVEMTLLRALAFH
PRMPLPEPEVPRQSFAPVAPTAVMTPTQVPPQPQSAPQQAPTVPLPETTSQVLAARQQLQ
RVQGATKAKKE

Sequence of entity 3 (E), FASTA

>8GIZ_3 DNA polymerase III subunit delta' (chains E)
MRWYPWLRPDFEKLVASYQAGRGHHALLIQALPGMGDDALIYALSRYLLCQQPQGHKSCG
HCRGCQLMQAGTHPDYYTLAPEKGKNTLGVDAVREVTEKLNEHARLGGAKVVWVTDAALL
TDAAANALLKTLEEPPAETWFFLATREPERLLATLRSRCRLHYLAPPPEQYAVTWLSREV
TMSQDALLAALRLSAGSPGAALALFQGDNWQARETLCQALAYSVPSGDWYSLLAALNHEQ
APARLHWLATLLMDALKRHHGAAQVTNVDVPGLVAELANHLSPSRLQAILGDVCHIREQL
MSVTGINRELLITDLLLRIEHYLQPGVVLPVPHL

Sequence of entity 4 (F), FASTA

>8GIZ_4 DNA polymerase III subunit psi (chains F)
MTSRRDWQLQQLGITQWSLRRPGALQGEIAIAIPAHVRLVMVANDLPALTDPLVSDVLRA
LTVSPDQVLQLTPEKIAMLPQGSHCNSWRLGTDEPLSLEGAQVASPALTDLRANPTARAA
LWQQICTYEHDFFPRND

Sequence of entity 5 (H, I), FASTA

>8GIZ_5 Beta sliding clamp (chains H, I)
MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLEMEMVARVALV
QPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVRSGRSRFSLSTLPAADFPNLD
DWQSEVEFTLPQATMKRLIEATQFSMAHQDVRYYLNGMLFETEGEELRTVATDGHRLAVC
SMPIGQSLPSHSVIVPRKGVIELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGR
FPDYRRVLPKNPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIEDAASQSAAYV
VMPMRL

Ligands and cofactors

ID	Name	Formula	Copies
AGS	Phosphothiophosphoric acid-adenylate ester	C10 H16 N5 O12 P3 S	3
MG	Magnesium ion	Mg	3
ZN	Zinc ion	Zn	4

Primary citation

Structural characterisation of the complete cycle of sliding clamp loading in Escherichia coli. Xu, Z.Q., Jergic, S., Lo, A.T.Y. et al. Nat Commun (2024) 15:8372-8372. DOI 10.1038/s41467-024-52623-9 · PubMed

Other PDB entries of the same protein (UniProt P28630 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1JQL 2.5 Å, Mechanism of Processivity Clamp Opening by the Delta Subunit Wrench of the Clamp Loader…
9OYJ 2.53 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYH 2.54 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYI 2.54 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
8GJ2 2.6 Å, E. coli clamp loader with closed clamp on primed template DNA
9OYK 2.6 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYM 2.6 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
1JR3 2.7 Å, Crystal Structure of the Processivity Clamp Loader Gamma Complex of E. coli DNA…
9OYN 2.7 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 10-nt gapped…
9OYC 2.71 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…
9OYE 2.72 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…
9OYD 2.73 Å, Structure of the E. coli clamp loader DnaX-complex loading beta-clamp onto 1-nt gapped…

Browse structure collections

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